Contacts of the helix formed by residues 514 - 535 (chain G) in PDB entry 3HR4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 514 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512G GLU* 3.5 10.1 - - + +
513G ILE* 1.3 93.7 - - - +
515G LEU* 1.3 65.8 + - - +
516G LYS* 3.4 31.9 - - + +
517G VAL* 3.7 10.5 + - + +
518G LEU* 3.6 15.6 + - - +
14H GLU* 4.1 15.5 - - - +
124H MET* 4.8 3.1 - - + +
127H GLU* 3.7 15.9 - - - +
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Residues in contact with LEU 515 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514G PRO* 1.3 68.9 - - - +
516G LYS* 1.3 61.3 + - - +
517G VAL 3.2 1.8 - - - -
518G LEU* 2.9 18.6 + - + +
519G VAL* 2.8 40.5 + - + +
92H PHE* 4.5 11.4 - - + -
105H LEU* 4.9 13.5 - - + -
124H MET* 3.8 34.7 - - + +
125H ILE* 4.8 5.4 - - + +
127H GLU* 2.9 20.9 + - + +
128H ALA* 5.0 5.8 - - + -
136H VAL* 5.3 10.8 - - + -
141H PHE* 5.6 4.0 - - + -
144H MET* 3.9 22.4 - - + -
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Residues in contact with LYS 516 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514G PRO* 3.4 27.4 - - + -
515G LEU* 1.3 74.2 - - - +
517G VAL* 1.3 59.9 + - + +
519G VAL* 3.1 11.8 - - + +
520G LYS* 2.8 42.6 + - - +
11H GLU* 3.8 31.6 - - + +
127H GLU* 3.3 38.2 + - - +
144H MET* 3.2 33.0 - - + +
145H MET* 5.5 0.4 - - - -
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Residues in contact with VAL 517 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513G ILE* 4.7 8.7 - - + -
514G PRO* 3.7 28.3 - - + +
516G LYS* 1.3 78.1 - - + +
518G LEU* 1.3 62.3 + - - +
520G LYS* 4.6 1.1 - - - -
521G ALA* 3.4 17.3 + - - +
11H GLU* 3.7 32.3 - - + +
14H GLU* 3.4 47.1 - - + +
15H ALA* 3.4 18.0 - - - +
18H LEU* 3.7 7.5 - - + +
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Residues in contact with LEU 518 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513G ILE* 5.3 4.0 - - + +
514G PRO 3.6 9.1 + - - +
515G LEU* 2.9 14.9 + - + +
517G VAL* 1.3 77.3 - - - +
519G VAL* 1.3 59.4 + - - +
520G LYS 3.0 1.3 - - - -
521G ALA* 2.6 29.3 + - + +
522G VAL* 2.9 15.8 + - + +
18H LEU* 4.2 16.2 - - + -
92H PHE* 4.0 28.7 - - + -
105H LEU* 4.2 9.9 - - + -
108H VAL* 4.7 8.7 - - + -
109H MET* 3.6 32.3 - - + -
112H LEU* 4.2 24.5 - - + -
124H MET* 5.4 0.9 - - - -
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Residues in contact with VAL 519 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515G LEU* 2.8 23.0 + - + +
516G LYS* 3.1 21.8 - - - +
518G LEU* 1.3 73.5 - - - +
520G LYS* 1.3 59.3 + - - +
522G VAL* 2.7 30.9 - - + +
523G LEU* 2.8 13.3 + - - +
85H ILE* 6.2 0.7 - - + -
88H ALA* 4.8 4.3 - - + -
92H PHE* 4.4 7.0 - - + -
141H PHE* 3.4 37.0 - - + -
144H MET* 4.2 7.0 - - + -
145H MET* 3.3 33.7 - - + -
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Residues in contact with LYS 520 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G LYS* 2.8 28.4 + - - +
517G VAL 4.0 4.5 - - - +
519G VAL* 1.3 76.4 - - + +
521G ALA* 1.3 64.7 + - - +
523G LEU* 3.0 22.5 - - + +
524G PHE* 3.0 9.5 + - - +
8H GLN* 4.1 14.8 + - - +
11H GLU* 2.6 46.1 + - + +
12H PHE* 3.7 44.6 - - + -
15H ALA* 4.4 8.5 - - + -
68H PHE* 6.1 0.7 - - - -
72H MET* 4.1 4.6 - - + +
76H MET* 4.2 13.5 - - + -
145H MET* 4.0 19.5 - - + +
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Residues in contact with ALA 521 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G VAL 3.4 11.9 + - - +
518G LEU* 2.6 17.7 + - + +
520G LYS* 1.3 74.2 - - - +
522G VAL* 1.3 62.3 + - - +
524G PHE* 3.1 12.3 + - - +
525G ALA 3.1 9.0 + - - -
15H ALA* 4.1 8.5 - - + +
18H LEU* 3.7 20.6 - - + -
19H PHE* 3.2 36.2 - - + -
68H PHE* 5.6 0.2 - - - -
112H LEU* 6.3 0.7 - - + -
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Residues in contact with VAL 522 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518G LEU* 2.9 13.1 + - + +
519G VAL* 2.7 40.6 - - + +
521G ALA* 1.3 76.7 - - - +
523G LEU* 1.3 63.1 + - - +
525G ALA* 3.1 8.0 + - - +
526G CYS* 3.0 31.6 + - - -
39H LEU* 4.7 18.4 - - + -
88H ALA* 3.9 12.6 - - + -
91H VAL* 3.4 33.7 - - + -
92H PHE* 4.2 13.0 - - + -
108H VAL* 6.5 1.6 - - + -
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Residues in contact with LEU 523 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519G VAL 2.8 13.6 + - - +
520G LYS* 3.0 15.3 - - - +
522G VAL* 1.3 78.6 - - - +
524G PHE* 1.3 54.8 + - - +
526G CYS* 2.9 20.3 + - - +
527G MET* 3.0 49.1 + - + +
72H MET* 4.5 0.9 - - + -
76H MET* 3.9 29.6 - - + -
84H GLU* 3.7 21.1 - - + -
85H ILE* 4.6 14.8 - - + +
88H ALA* 4.3 10.3 - - + -
145H MET* 3.3 28.3 - - + -
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Residues in contact with PHE 524 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520G LYS 3.0 6.0 + - - +
521G ALA* 3.3 8.1 - - - +
523G LEU* 1.3 81.3 - - - +
525G ALA* 1.3 59.7 + - - +
526G CYS 3.3 0.7 + - - -
527G MET* 3.3 19.8 + - - +
528G LEU* 3.4 39.3 + - + +
19H PHE* 3.3 37.0 - + + -
27H ILE* 5.1 4.5 - - + -
32H LEU* 4.4 5.2 - - + -
55H VAL* 4.6 11.4 - - + -
63H ILE* 4.8 11.9 - - + -
68H PHE* 3.6 33.2 - + + -
71H MET* 3.5 28.3 - - + -
72H MET* 3.5 29.6 - - + +
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Residues in contact with ALA 525 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521G ALA 3.1 10.2 + - - +
522G VAL* 3.1 8.3 + - - +
524G PHE* 1.3 80.7 - - - +
526G CYS* 1.3 60.3 + - - +
528G LEU* 4.0 2.2 + - - -
529G MET* 3.2 20.4 + - - +
19H PHE* 4.3 10.1 - - + -
36H MET* 3.3 31.0 - - + +
39H LEU* 3.5 31.4 - - + -
41H GLN* 3.7 3.3 + - - +
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Residues in contact with CYS 526 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522G VAL* 3.0 24.9 + - - -
523G LEU* 2.9 9.9 + - - +
525G ALA* 1.3 77.4 - - - +
527G MET* 1.3 57.3 + - - +
529G MET* 4.3 1.8 - - - +
530G ARG* 2.6 37.9 + - - +
41H GLN* 3.7 19.3 - - - -
84H GLU* 3.9 8.1 - - - +
87H GLU* 3.9 31.5 - - + +
88H ALA* 4.1 24.5 - - - -
91H VAL* 4.7 2.9 - - - -
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Residues in contact with MET 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523G LEU* 3.0 34.1 + - + +
524G PHE* 3.4 14.1 - - + +
526G CYS* 1.3 81.2 - - - +
528G LEU* 1.3 66.9 + - + +
530G ARG* 3.2 2.7 + - - +
531G LYS* 3.0 21.5 + - - +
71H MET* 4.9 8.7 - - + -
72H MET* 3.6 33.0 - - + -
75H LYS* 3.2 45.1 - - + -
76H MET* 4.8 4.9 - - + -
84H GLU* 3.4 38.8 + - - +
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Residues in contact with LEU 528 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524G PHE* 3.4 41.5 - - + +
525G ALA* 4.0 4.5 - - - +
527G MET* 1.3 82.7 - - + +
529G MET* 1.3 61.4 + - - +
531G LYS* 3.4 5.9 + - + +
532G THR* 3.3 26.5 + - - +
32H LEU* 4.1 20.6 - - + -
36H MET* 4.4 3.1 - - + -
51H MET* 3.3 40.1 - - + +
54H GLU* 5.3 7.2 - - + +
55H VAL* 4.1 11.9 - - + -
63H ILE* 6.0 0.7 - - + -
71H MET* 4.1 26.2 - - + -
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Residues in contact with MET 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525G ALA 3.2 16.8 + - - +
526G CYS* 3.1 3.9 + - - +
528G LEU* 1.3 76.8 - - - +
530G ARG* 1.3 67.4 + - - +
532G THR* 3.6 17.3 - - - +
533G MET* 2.9 41.3 + - + +
536G ARG* 3.7 26.0 - - - +
36H MET* 3.4 19.0 - - + +
41H GLN* 3.4 30.5 - - + +
42H ASN 4.9 0.4 - - - -
43H PRO* 3.6 28.3 - - + -
47H GLU* 4.6 0.2 - - - +
87H GLU* 5.2 2.7 - - - +
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Residues in contact with ARG 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526G CYS 2.6 20.9 + - - +
527G MET 3.6 3.6 - - - +
529G MET* 1.3 72.5 - - - +
531G LYS* 1.3 59.3 + - - +
533G MET* 2.9 8.0 - - - +
534G ALA* 2.8 34.0 + - + +
80H ASP* 3.4 20.4 + - - -
83H GLU* 3.1 29.9 + - - +
84H GLU* 2.7 49.9 + - - +
86H ARG* 5.9 0.2 - - - +
87H GLU* 3.6 29.4 + - - +
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Residues in contact with LYS 531 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527G MET 3.0 13.2 + - - +
528G LEU* 3.5 11.9 - - - +
529G MET 3.2 0.2 - - - -
530G ARG* 1.3 72.6 - - - +
532G THR* 1.3 62.1 + - + +
533G MET 2.5 16.6 + - - -
534G ALA* 2.9 17.6 + - - +
535G SER* 3.3 15.7 + - - +
54H GLU* 2.7 35.2 + - - +
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Residues in contact with THR 532 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528G LEU 3.3 11.0 + - - +
529G MET* 3.6 16.0 - - - +
531G LYS* 1.3 81.4 - - + +
533G MET* 1.3 55.6 + - - +
535G SER* 3.6 14.8 + - - +
536G ARG* 3.8 11.3 + - - +
43H PRO* 4.8 0.3 - - - +
47H GLU* 3.3 36.8 + - + +
50H ASP* 4.8 7.2 - - + -
51H MET* 3.8 21.0 - - + +
54H GLU* 3.7 24.0 - - - +
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Residues in contact with MET 533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529G MET* 2.9 39.2 + - + +
530G ARG* 2.9 11.4 - - - +
531G LYS 2.5 6.3 + - - -
532G THR* 1.3 74.5 - - - +
534G ALA* 1.3 51.9 + - - +
535G SER 2.9 4.5 - - - -
536G ARG* 2.7 69.5 + - - +
565G PHE 4.9 2.2 - - - +
566G ASN* 4.4 31.1 + - - +
42H ASN* 5.9 2.2 - - - +
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Residues in contact with ALA 534 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530G ARG* 2.8 17.6 + - + +
531G LYS* 2.9 8.5 + - - +
533G MET* 1.3 77.0 - - - +
535G SER* 1.3 57.4 + - - +
536G ARG 3.3 4.7 + - - +
566G ASN* 5.7 2.7 - - - +
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Residues in contact with SER 535 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531G LYS* 3.3 10.4 + - - +
532G THR* 3.6 22.5 + - - +
533G MET 2.9 1.4 - - - -
534G ALA* 1.3 75.5 - - - +
536G ARG* 1.3 64.2 + - - +
537G VAL 4.0 0.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il